From mboxrd@z Thu Jan 1 00:00:00 1970 From: Xebar Saram Subject: Re: helm-bibtex questions Date: Sat, 27 Jun 2015 09:11:59 +0300 Message-ID: References: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=089e01493b94feb7f4051979bb96 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:60444) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z8jLR-00061D-E7 for emacs-orgmode@gnu.org; Sat, 27 Jun 2015 02:12:09 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z8jLN-0001zm-1L for emacs-orgmode@gnu.org; Sat, 27 Jun 2015 02:12:05 -0400 Received: from mail-la0-x22a.google.com ([2a00:1450:4010:c03::22a]:33030) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z8jLM-0001yg-BQ for emacs-orgmode@gnu.org; Sat, 27 Jun 2015 02:12:00 -0400 Received: by laar3 with SMTP id r3so14808457laa.0 for ; Fri, 26 Jun 2015 23:11:59 -0700 (PDT) In-Reply-To: List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: John Kitchin Cc: org mode --089e01493b94feb7f4051979bb96 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable hmm strange still dosent work for me. here is the top section of my bib fil= e -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*- @article{ackerman-1998-discr-clear, author =3D {Ackerman, {S.A.} and Strabala, {K.I.} and Menzel, {W.P.} and Frey, {R.A.} and Moeller, {C.C.} and Gumley, {L.E.}}, title =3D {Discriminating Clear Sky From Clouds With Modis}, journal =3D {Journal of Geophysical Research}, volume =3D 103, number =3D {D24}, pages =3D {32,141--32,157}, year =3D 1998, shorttitle =3D {Discriminating clear sky from clouds with {MODIS}}, } when i use the org ref clean i still get bibtex-format-entry: Mandatory field `journal' is missing also in the emacs menu the entry type is still bibtex. i tried restarting emacs and still no go. any clue? also do you prefer I continue this discussion on the github org-ref site? best! Z On Fri, Jun 26, 2015 at 5:28 PM, John Kitchin wrote: > > http://tex.stackexchange.com/questions/78455/does-emacs-support-editing-b= ibliography-files-for-biblatex > > I think you need this in your bibtex file: > > -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*- > > > Xebar Saram writes: > > > thanks so much again John > > > > i did add this line > > (bibtex-set-dialect 'biblatex) > > in my init but that dosent seem to do much as i still get the "journal > > mandatory field missing" error. anything else i can try? > > > > best > > > > Z > > > > > > On Thu, Jun 25, 2015 at 2:09 PM, John Kitchin > > wrote: > > > >> I believe that is an emacs bibtex issue. You need some kind of line in > >> your bibtex file to specify it is the biblatex dialect. > >> > >> > >> On June 25, 2015, at 6:58 AM, Xebar Saram wrote: > >> > >> > >> Great, works well. one question though (and this may very well be due = to > >> my inexperience). the jabref export i had used 'journaltitle' instead = of > >> journal to be (to my understanding) compatible with the newer .bib fil= es > >> used by biblatex (and biber). when i ran org-ref clean it gave an erro= r > on" > >> journal mandatory field missing". i had to replace all 'journaltitle' > to > >> 'journal' to get it to work. > >> is this by design? does org-ref not support the new biblatex/biber .bi= b > >> file format? > >> > >> kind regards > >> > >> Itai > >> > >> On Thu, Jun 25, 2015 at 12:03 AM, John Kitchin > > >> wrote: > >> > >>> yes, there is a way ;) > >>> > >>> First. Make sure you have a backup of the references. I like to keep > >>> mine in a local git repo so you can undo any mistakes that get made. > >>> > >>> I suggest you run these first: > >>> %% (bibtex-validate-globally) ; checks for duplicate keys > >>> %% (bibtex-validate) > >>> > >>> I also recommend you run bibtex-sort (it is easier to spot duplicates > in > >>> a sorted list). > >>> > >>> and (org-ref-build-full-bibliography) <- makes a pdf of all reference= s. > >>> > >>> to make sure everything is compliant and functional. > >>> > >>> Then, put this next line at the top of your bibtex file. The t > argument to > >>> org-ref-clean-bibtex-entry will preserve your existing keys. > >>> > >>> % (bibtex-map-entries (lambda (key start end) > (org-ref-clean-bibtex-entry > >>> t))) > >>> > >>> Put your cursor at the end of that line, and type C-x C-e to run the > >>> function, and > >>> wait patiently. It took a few minutes on my 1300 entries, and I had t= o > >>> restart it once on some entry. > >>> > >>> when it is done, run (org-ref-build-full-bibliography) again to make > >>> sure it works and review the ~200 page pdf ;). fix errors and repeat > >>> until it builds ;) > >>> > >>> Note if you want to change title cases in all entries you can use > >>> > >>> % (bibtex-map-entries 'jmax-title-case-article) > >>> % (bibtex-map-entries 'jmax-sentence-case-article) > >>> > >>> I hope that helps! > >>> > >>> Xebar Saram writes: > >>> > >>> > John > >>> > > >>> > First of all thanks so much for the excellent > org-ref-clean-bibtex-entry > >>> > function i love it! > >>> > also your blog post on cleaning the bib file is a life saver > >>> > > >>> > i have 800 references, is there a way to auto > >>> > make org-ref-clean-bibtex-entry go thorough my whole bib file inste= ad > >>> of me > >>> > going and cleaning it 1 by 1? > >>> > > >>> > kind regards > >>> > > >>> > Z. > >>> > > >>> > On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg < > >>> malsburg@posteo.de> > >>> > wrote: > >>> > > >>> >> > >>> >> > >>> >> Here is my CV in org-mode: > >>> >> > >>> >> https://gist.github.com/tmalsburg/96084ba82281937c26b7 > >>> >> > >>> >> It=E2=80=99s a pretty straightforward org document except for one = thing: the > >>> key > >>> >> to making this work was biblatex which can be used to create sever= al > >>> >> lists of references filtered according to keywords, author, etc. > This > >>> >> allowed me to have separate sections for journal articles, > conference > >>> >> presentations, etc. I store the relevant keywords in the tags > field of > >>> >> the BibTeX entries and since biblatex doesn=E2=80=99t know this fi= eld, I > copy > >>> >> the tags on-the-fly to the keywords field (see DeclareSourcemap in > the > >>> >> LaTeX headers). > >>> >> > >>> >> Titus > >>> >> > >>> >> On 2015-06-22 Mon 07:28, Xebar Saram wrote: > >>> >> > Hi John > >>> >> > > >>> >> > a bit off topic, but do you also write your academic CV in > orgmode or > >>> >> > lateX? in anycase would you mind sharing your org/latex CV > template? > >>> it > >>> >> > would be helpful as a starting point for me if thats possible. > >>> >> > > >>> >> > kind regards and thanks so much in advance > >>> >> > > >>> >> > Z > >>> >> > > >>> >> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin < > >>> jkitchin@andrew.cmu.edu> > >>> >> > wrote: > >>> >> > > >>> >> >> sweet! I did not know you could do that! I will be refactoring > >>> org-ref > >>> >> >> soon to do that instead of redefining the commands! > >>> >> >> > >>> >> >> John > >>> >> >> > >>> >> >> ----------------------------------- > >>> >> >> Professor John Kitchin > >>> >> >> Doherty Hall A207F > >>> >> >> Department of Chemical Engineering > >>> >> >> Carnegie Mellon University > >>> >> >> Pittsburgh, PA 15213 > >>> >> >> 412-268-7803 > >>> >> >> @johnkitchin > >>> >> >> http://kitchingroup.cheme.cmu.edu > >>> >> >> > >>> >> >> > >>> >> >> On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg < > >>> >> >> malsburg@posteo.de> wrote: > >>> >> >> > >>> >> >>> > >>> >> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote: > >>> >> >>> > Hi again Titus > >>> >> >>> > > >>> >> >>> > 2 quick questions that arose from using helm-bitex today > >>> extensively: > >>> >> >>> > > >>> >> >>> > how does one exclude in the search items? for example i want > to > >>> >> search > >>> >> >>> for > >>> >> >>> > xebar without keyword "progress" (I want to exclude in > progress > >>> >> articles > >>> >> >>> > not published yet) > >>> >> >>> > > >>> >> >>> > is it possible to define default enter command in helm-bibte= x > ? > >>> >> >>> > >>> >> >>> Yes. Helm uses the first action as the default action. To > move an > >>> >> >>> action to the top of the list you can use the following code: > >>> >> >>> > >>> >> >>> (helm-delete-action-from-source "Insert BibTeX key" > >>> >> helm-source-bibtex) > >>> >> >>> (helm-add-action-to-source "Insert BibTeX key" > >>> >> 'helm-bibtex-insert-key > >>> >> >>> helm-source-bibtex 0) > >>> >> >>> > >>> >> >>> The second argument in the second line is the function that > >>> executes > >>> >> the > >>> >> >>> action. Here is a list of all actions and their functions: > >>> >> >>> > >>> >> >>> Open PDF file (if present): helm-bibtex-open-pdf > >>> >> >>> Open URL or DOI in browser: helm-bibtex-open-url-or-doi > >>> >> >>> Insert citation: helm-bibtex-insert-citation > >>> >> >>> Insert reference: helm-bibtex-insert-reference > >>> >> >>> Insert BibTeX key: helm-bibtex-insert-key > >>> >> >>> Insert BibTeX entry: helm-bibtex-insert-bibtex > >>> >> >>> Attach PDF to email: helm-bibtex-add-PDF-attachment > >>> >> >>> Edit notes: helm-bibtex-edit-notes > >>> >> >>> Show entry: helm-bibtex-show-entry > >>> >> >>> > >>> >> >>> Best, > >>> >> >>> > >>> >> >>> Titus > >>> >> >>> > >>> >> >>> > > >>> >> >>> > best > >>> >> >>> > > >>> >> >>> > Z > >>> >> >>> > > >>> >> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg < > >>> >> >>> malsburg@posteo.de> > >>> >> >>> > wrote: > >>> >> >>> > > >>> >> >>> >> > >>> >> >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote: > >>> >> >>> >> > Hi Titus and thx so much for the answers! > >>> >> >>> >> > > >>> >> >>> >> > i will in the future use the github page to make requests= . > >>> >> >>> >> > > >>> >> >>> >> > "The number of matches will be displayed in the mode line= . > " > >>> >> >>> >> > > >>> >> >>> >> > i see that now thx! :) the problem was(is) that its color= ed > >>> black > >>> >> on > >>> >> >>> my > >>> >> >>> >> > black modline BG which makes it invisible ;-) i assume > thats > >>> an > >>> >> helm > >>> >> >>> >> config > >>> >> >>> >> > i need to change > >>> >> >>> >> > > >>> >> >>> >> > > >>> >> >>> >> > "If you don=E2=80=99t want to type these search expressio= ns, you > could > >>> >> >>> create a > >>> >> >>> >> > command that invokes helm-bibtex with a default search > >>> expression > >>> >> and > >>> >> >>> >> that > >>> >> >>> >> > command could be bound to a keyboard shortcut." > >>> >> >>> >> > > >>> >> >>> >> > that would be prefect for me and a solution to my issue. > >>> would you > >>> >> >>> mind > >>> >> >>> >> > giving an example of such a code chunk. unfortunately i > dont > >>> know > >>> >> >>> elisp > >>> >> >>> >> though > >>> >> >>> >> > as john recommended i will do my best this summer when th= e > >>> >> semester > >>> >> >>> ends > >>> >> >>> >> to > >>> >> >>> >> > try and pick it up :) > >>> >> >>> >> > >>> >> >>> >> Sure, here you go: > >>> >> >>> >> > >>> >> >>> >> #+BEGIN_SRC elisp > >>> >> >>> >> ;; Define helm-search with predefined search expression: > >>> >> >>> >> (defun helm-bibtex-my-publications () > >>> >> >>> >> "Search BibTeX entries authored by Xebar Saram." > >>> >> >>> >> (interactive) > >>> >> >>> >> (helm :sources '(helm-source-bibtex) > >>> >> >>> >> :full-frame t > >>> >> >>> >> :input "xebar saram" > >>> >> >>> >> :candidate-number-limit 500)) > >>> >> >>> >> > >>> >> >>> >> ;; Bind this search function to Ctrl-x p: > >>> >> >>> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications) > >>> >> >>> >> #+END_SRC > >>> >> >>> >> > >>> >> >>> >> > i will definitely use your tag system as you recommended, > >>> sounds > >>> >> >>> perfect > >>> >> >>> >> > for me > >>> >> >>> >> > >>> >> >>> >> The tag system also comes in handy when generating > publication > >>> lists > >>> >> >>> for > >>> >> >>> >> CVs and web pages because BibTeX does not distinguish betwe= en > >>> >> >>> conference > >>> >> >>> >> papers, posters, and talks. If you have tags for that, it= =E2=80=99s > >>> >> relatively > >>> >> >>> >> easy to create separate sections for these types of > publications > >>> >> using > >>> >> >>> >> biblatex or bib2bib and bibtex2html in the case of web page= s. > >>> >> >>> >> > >>> >> >>> >> > thanks again for your kind help and the amazing app ;-) > >>> >> >>> >> > >>> >> >>> >> You are welcome. > >>> >> >>> >> > >>> >> >>> >> Titus > >>> >> >>> >> > >>> >> >>> >> > > >>> >> >>> >> > best > >>> >> >>> >> > > >>> >> >>> >> > Z > >>> >> >>> >> > > >>> >> >>> >> > > >>> >> >>> >> > > >>> >> >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg = < > >>> >> >>> >> malsburg@posteo.de > >>> >> >>> >> >> wrote: > >>> >> >>> >> > > >>> >> >>> >> >> > >>> >> >>> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote: > >>> >> >>> >> >> > Hi Titus > >>> >> >>> >> >> > > >>> >> >>> >> >> > I have been exploring helm-bibtex a bit today and have > some > >>> >> >>> questions. > >>> >> >>> >> >> btw > >>> >> >>> >> >> > is this the preferred way to make requests/ask questio= ns > >>> or is > >>> >> >>> >> >> > github preferred? > >>> >> >>> >> >> > >>> >> >>> >> >> Helm-bibtex is not part of org (although it tries to wor= k > >>> well > >>> >> with > >>> >> >>> >> >> org). So I=E2=80=99m not sure whether this list is the = best place > >>> for > >>> >> >>> >> >> discussing it. For now the issue tracker on Github migh= t > be > >>> a > >>> >> >>> better > >>> >> >>> >> >> option: > >>> >> >>> >> >> > >>> >> >>> >> >> https://github.com/tmalsburg/helm-bibtex/issues > >>> >> >>> >> >> > >>> >> >>> >> >> > in any case i was wondering a few things: > >>> >> >>> >> >> > > >>> >> >>> >> >> > 1. is it possible to have custom sorting? i want all > views > >>> to > >>> >> >>> sort by > >>> >> >>> >> >> > Author, year, month > >>> >> >>> >> >> > >>> >> >>> >> >> I prefer to see the entries in the (inverse) order in > which > >>> they > >>> >> >>> appear > >>> >> >>> >> >> in the BibTeX file. This way, recent additions show up = at > >>> the > >>> >> >>> >> >> top. However, I agree that sorting would be useful (see > >>> issues > >>> >> #5 > >>> >> >>> and > >>> >> >>> >> >> #21); it just doesn=E2=80=99t have high priority for me.= Pull > >>> requests > >>> >> >>> welcome. > >>> >> >>> >> >> > >>> >> >>> >> >> > 2. i would really like a way to have stored smart grou= ps > >>> (like > >>> >> the > >>> >> >>> >> jabref > >>> >> >>> >> >> > dynamic groups if your aware of that). that is for > example > >>> >> create > >>> >> >>> a > >>> >> >>> >> group > >>> >> >>> >> >> > that auto selects all publications i have (by my > first/last > >>> >> name) > >>> >> >>> and > >>> >> >>> >> >> shows > >>> >> >>> >> >> > the count (in numbers) of these publications. > >>> >> >>> >> >> > >>> >> >>> >> >> I=E2=80=99m not familiar with smart groups but it seems = that all > >>> >> >>> helm-bibtex is > >>> >> >>> >> >> doing is giving you very flexible smart groups defined b= y > >>> your > >>> >> >>> search > >>> >> >>> >> >> expressions. For example, if you want a list of your > >>> >> publications, > >>> >> >>> you > >>> >> >>> >> >> can simple enter your name. And if you want a list of > your > >>> >> >>> articles, > >>> >> >>> >> >> you can enter your name + =E2=80=9Carticle=E2=80=9D. If= you want all your > >>> >> articles > >>> >> >>> from > >>> >> >>> >> >> 2010, enter your name + =E2=80=9Carticles 2010=E2=80=9D.= And so on. The > >>> number > >>> >> of > >>> >> >>> >> >> matches will be displayed in the mode line. If you don= =E2=80=99t > >>> want to > >>> >> >>> type > >>> >> >>> >> >> these search expressions, you could create a command tha= t > >>> invokes > >>> >> >>> >> >> helm-bibtex with a default search expression and that > command > >>> >> could > >>> >> >>> be > >>> >> >>> >> >> bound to a keyboard shortcut. > >>> >> >>> >> >> > >>> >> >>> >> >> > Another example is a group to keep track of all the > papers > >>> im > >>> >> >>> working > >>> >> >>> >> on > >>> >> >>> >> >> or > >>> >> >>> >> >> > invloved with by matching keyword author and prep/*oth= er > >>> key > >>> >> word > >>> >> >>> >> >> > >>> >> >>> >> >> I use two BibTeX fields to tag entries: =E2=80=9Ckeyword= s=E2=80=9D for > >>> keywords > >>> >> >>> >> >> describing the content of the paper (as usual) and =E2= =80=9Ctags=E2=80=9D > for > >>> >> meta > >>> >> >>> >> >> data. Values that I use in tags are =E2=80=9Cown=E2=80= =9D, =E2=80=9Cmanuscript=E2=80=9D, > >>> >> =E2=80=9Cposter=E2=80=9D, > >>> >> >>> >> >> =E2=80=9Ctalk=E2=80=9D, =E2=80=A6 So if I want a list of= all articles in > progress, I > >>> >> search > >>> >> >>> for > >>> >> >>> >> >> =E2=80=9Cown manuscript=E2=80=9D. Since the tags field = is non-standard, > it > >>> has > >>> >> to > >>> >> >>> be > >>> >> >>> >> >> added to `helm-bibtex-additional-search-fields`. > >>> >> >>> >> >> > >>> >> >>> >> >> Another solution would be to use the pubstate field and = to > >>> search > >>> >> >>> for > >>> >> >>> >> >> your name and =E2=80=9Cforthcoming=E2=80=9D (add pubstat= e to > >>> >> >>> >> >> helm-bibtex-additional-search-fields for this to work). > >>> >> >>> >> >> > >>> >> >>> >> >> > 3.is it possible to ass an option to auto generate a > >>> bibkey > >>> >> for a > >>> >> >>> >> >> selected > >>> >> >>> >> >> > citation based on user criteria such as > >>> >> author(date)short-title? > >>> >> >>> >> >> > >>> >> >>> >> >> Maintaining the content of the BibTeX file not really in > the > >>> >> scope > >>> >> >>> of > >>> >> >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand= ). > >>> >> Perhaps > >>> >> >>> >> >> org-ref or ebib can help here? Once you have a function > that > >>> >> >>> generates > >>> >> >>> >> >> a new key and inserts it in the BibTeX file, you can > easily > >>> add > >>> >> it > >>> >> >>> to > >>> >> >>> >> >> the list of actions in helm-bibtex. > >>> >> >>> >> >> > >>> >> >>> >> >> Hope that helps. > >>> >> >>> >> >> > >>> >> >>> >> >> Titus > >>> >> >>> >> >> > >>> >> >>> >> >> > thx so much in advance, you and john have given me > >>> confidence > >>> >> to > >>> >> >>> >> finally > >>> >> >>> >> >> > dive into the whole latex/bibteX world > >>> >> >>> >> >> > > >>> >> >>> >> >> > best > >>> >> >>> >> >> > > >>> >> >>> >> >> > Z > >>> >> >>> >> >> > >>> >> >>> >> >> > >>> >> >>> >> > >>> >> >>> >> > >>> >> >>> > >>> >> >>> > >>> >> >> > >>> >> > >>> >> > >>> > >>> -- > >>> Professor John Kitchin > >>> Doherty Hall A207F > >>> Department of Chemical Engineering > >>> Carnegie Mellon University > >>> Pittsburgh, PA 15213 > >>> 412-268-7803 > >>> @johnkitchin > >>> http://kitchingroup.cheme.cmu.edu > >>> > >> > >> > > -- > Professor John Kitchin > Doherty Hall A207F > Department of Chemical Engineering > Carnegie Mellon University > Pittsburgh, PA 15213 > 412-268-7803 > @johnkitchin > http://kitchingroup.cheme.cmu.edu > --089e01493b94feb7f4051979bb96 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
hmm strange still dosent work for me. here is the top sect= ion of my bib file

-*- mode:bibtex; eval: (bibtex-s= et-dialect 'biblatex); -*-

@article{ackerm= an-1998-discr-clear,
=C2=A0 author =3D {Ackerman, {S.A.} and Strabala, {K.I.} and Menzel,=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 {= W.P.} and Frey, {R.A.} and Moeller, {C.C.} and
=C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Gumley, {L.E.}},
= =C2=A0 title =3D {Discri= minating Clear Sky From Clouds With Modis},
=C2=A0 journal =3D {Journal of Geophysical Re= search},
=C2=A0 volume =3D 103,
=C2=A0 number =3D {D24},
=C2=A0 pages =3D {32,141--32,157},
=C2=A0 year =3D= 1998,
=C2=A0 = shorttitle =3D {Discrimi= nating clear sky from clouds with {MODIS}},
}

when i use the org ref clean i still get=C2=A0

bibtex-format-entry: Mandatory field `journal&= #39; is missing


also in the e= macs menu the entry type is still bibtex. i tried restarting emacs and stil= l no go.

any clue? also do you prefer I continue t= his discussion on the github org-ref site?

best!

Z


On Fri, Jun 26, 2015 at 5:28 PM, John Ki= tchin <jkitchin@andrew.cmu.edu> wrote:
http://tex.stackexchange.com/questions/78455/does-ema= cs-support-editing-bibliography-files-for-biblatex

I think you need this in your bibtex file:

-*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-


Xebar Saram writes:

> thanks so much again John
>
> i did add this line
> (bibtex-set-dialect 'biblatex)
> in my init but that dosent seem to do much as i still get the "jo= urnal
> mandatory field missing" error. anything else i can try?
>
> best
>
> Z
>
>
> On Thu, Jun 25, 2015 at 2:09 PM, John Kitchin <johnrkitchin@gmail.com>
> wrote:
>
>> I believe that is an emacs bibtex issue. You need some kind of lin= e in
>> your bibtex file to specify it is the biblatex dialect.
>>
>>
>> On June 25, 2015, at 6:58 AM, Xebar Saram <zeltakc@gmail.com> wrote:
>>
>>
>> Great, works well. one question though (and this may very well be = due to
>> my inexperience). the jabref export i had used 'journaltitle&#= 39; instead of
>> journal to be (to my understanding) compatible with the newer .bib= files
>> used by biblatex (and biber). when i ran org-ref clean it gave an = error on"
>> journal mandatory field missing". i had to replace all 'j= ournaltitle'=C2=A0 to
>> 'journal' to get it to work.
>> is this by design? does org-ref not support the new biblatex/biber= .bib
>> file format?
>>
>> kind regards
>>
>> Itai
>>
>> On Thu, Jun 25, 2015 at 12:03 AM, John Kitchin <jkitchin@andrew.cmu.edu>
>> wrote:
>>
>>> yes, there is a way ;)
>>>
>>> First. Make sure you have a backup of the references. I like t= o keep
>>> mine in a local git repo so you can undo any mistakes that get= made.
>>>
>>> I suggest you run these first:
>>> %% (bibtex-validate-globally)=C2=A0 =C2=A0; checks for duplica= te keys
>>> %% (bibtex-validate)
>>>
>>> I also recommend you run bibtex-sort (it is easier to spot dup= licates in
>>> a sorted list).
>>>
>>> and (org-ref-build-full-bibliography) <- makes a pdf of all= references.
>>>
>>> to make sure everything is compliant and functional.
>>>
>>> Then, put this next line at the top of your bibtex file. The t= argument to
>>> org-ref-clean-bibtex-entry will preserve your existing keys. >>>
>>> % (bibtex-map-entries (lambda (key start end) (org-ref-clean-b= ibtex-entry
>>> t)))
>>>
>>> Put your cursor at the end of that line, and type C-x C-e to r= un the
>>> function, and
>>> wait patiently. It took a few minutes on my 1300 entries, and = I had to
>>> restart it once on some entry.
>>>
>>> when it is done, run (org-ref-build-full-bibliography) again t= o make
>>> sure it works and review the ~200 page pdf ;). fix errors and = repeat
>>> until it builds ;)
>>>
>>> Note if you want to change title cases in all entries you can = use
>>>
>>> % (bibtex-map-entries 'jmax-title-case-article)
>>> % (bibtex-map-entries 'jmax-sentence-case-article)
>>>
>>> I hope that helps!
>>>
>>> Xebar Saram writes:
>>>
>>> > John
>>> >
>>> > First of all thanks so much for the excellent org-ref-cle= an-bibtex-entry
>>> > function i love it!
>>> > also your blog post on cleaning the bib file is a life sa= ver
>>> >
>>> > i have 800 references, is there a way to auto
>>> > make org-ref-clean-bibtex-entry go thorough my whole bib = file instead
>>> of me
>>> > going and cleaning it 1 by 1?
>>> >
>>> > kind regards
>>> >
>>> > Z.
>>> >
>>> > On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg &= lt;
>>> malsburg@posteo.de&g= t;
>>> > wrote:
>>> >
>>> >>
>>> >>
>>> >> Here is my CV in org-mode:
>>> >>
>>> >>=C2=A0 =C2=A0https://gist= .github.com/tmalsburg/96084ba82281937c26b7
>>> >>
>>> >> It=E2=80=99s a pretty straightforward org document ex= cept for one thing: the
>>> key
>>> >> to making this work was biblatex which can be used to= create several
>>> >> lists of references filtered according to keywords, a= uthor, etc.=C2=A0 This
>>> >> allowed me to have separate sections for journal arti= cles, conference
>>> >> presentations, etc.=C2=A0 I store the relevant keywor= ds in the tags field of
>>> >> the BibTeX entries and since biblatex doesn=E2=80=99t= know this field, I copy
>>> >> the tags on-the-fly to the keywords field (see Declar= eSourcemap in the
>>> >> LaTeX headers).
>>> >>
>>> >>=C2=A0 =C2=A0Titus
>>> >>
>>> >> On 2015-06-22 Mon 07:28, Xebar Saram wrote:
>>> >> > Hi John
>>> >> >
>>> >> > a bit off topic, but do you also write your acad= emic CV in orgmode or
>>> >> > lateX? in anycase would you mind sharing your or= g/latex CV template?
>>> it
>>> >> > would be helpful as a starting point for me if t= hats possible.
>>> >> >
>>> >> > kind regards and thanks so much in advance
>>> >> >
>>> >> > Z
>>> >> >
>>> >> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin &l= t;
>>> jkitchin@andrew.cmu= .edu>
>>> >> > wrote:
>>> >> >
>>> >> >> sweet! I did not know you could do that! I w= ill be refactoring
>>> org-ref
>>> >> >> soon to do that instead of redefining the co= mmands!
>>> >> >>
>>> >> >> John
>>> >> >>
>>> >> >> -----------------------------------
>>> >> >> Professor John Kitchin
>>> >> >> Doherty Hall A207F
>>> >> >> Department of Chemical Engineering
>>> >> >> Carnegie Mellon University
>>> >> >> Pittsburgh, PA 15213
>>> >> >> 412-268-7803
>>> >> >> @johnkitchin
>>> >> >> http://kitchingroup.cheme.cmu.edu
>>> >> >>
>>> >> >>
>>> >> >> On Sun, Jun 21, 2015 at 2:29 PM, Titus von d= er Malsburg <
>>> >> >> malsbu= rg@posteo.de> wrote:
>>> >> >>
>>> >> >>>
>>> >> >>> On 2015-06-19 Fri 03:56, Xebar Saram wro= te:
>>> >> >>> > Hi again Titus
>>> >> >>> >
>>> >> >>> > 2 quick questions that arose from u= sing helm-bitex today
>>> extensively:
>>> >> >>> >
>>> >> >>> > how does one exclude in the search = items? for example i want to
>>> >> search
>>> >> >>> for
>>> >> >>> > xebar without keyword "progres= s" (I want to exclude in progress
>>> >> articles
>>> >> >>> > not published yet)
>>> >> >>> >
>>> >> >>> > is it possible to define default en= ter command in helm-bibtex ?
>>> >> >>>
>>> >> >>> Yes.=C2=A0 Helm uses the first action as= the default action.=C2=A0 To move an
>>> >> >>> action to the top of the list you can us= e the following code:
>>> >> >>>
>>> >> >>>=C2=A0 =C2=A0(helm-delete-action-from-sou= rce "Insert BibTeX key"
>>> >> helm-source-bibtex)
>>> >> >>>=C2=A0 =C2=A0(helm-add-action-to-source &= quot;Insert BibTeX key"
>>> >> 'helm-bibtex-insert-key
>>> >> >>> helm-source-bibtex 0)
>>> >> >>>
>>> >> >>> The second argument in the second line i= s the function that
>>> executes
>>> >> the
>>> >> >>> action.=C2=A0 Here is a list of all acti= ons and their functions:
>>> >> >>>
>>> >> >>>=C2=A0 =C2=A0Open PDF file (if present): = helm-bibtex-open-pdf
>>> >> >>>=C2=A0 =C2=A0Open URL or DOI in browser: = helm-bibtex-open-url-or-doi
>>> >> >>>=C2=A0 =C2=A0Insert citation: helm-bibtex= -insert-citation
>>> >> >>>=C2=A0 =C2=A0Insert reference: helm-bibte= x-insert-reference
>>> >> >>>=C2=A0 =C2=A0Insert BibTeX key: helm-bibt= ex-insert-key
>>> >> >>>=C2=A0 =C2=A0Insert BibTeX entry: helm-bi= btex-insert-bibtex
>>> >> >>>=C2=A0 =C2=A0Attach PDF to email: helm-bi= btex-add-PDF-attachment
>>> >> >>>=C2=A0 =C2=A0Edit notes: helm-bibtex-edit= -notes
>>> >> >>>=C2=A0 =C2=A0Show entry: helm-bibtex-show= -entry
>>> >> >>>
>>> >> >>> Best,
>>> >> >>>
>>> >> >>>=C2=A0 =C2=A0Titus
>>> >> >>>
>>> >> >>> >
>>> >> >>> > best
>>> >> >>> >
>>> >> >>> > Z
>>> >> >>> >
>>> >> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Ti= tus von der Malsburg <
>>> >> >>> ma= lsburg@posteo.de>
>>> >> >>> > wrote:
>>> >> >>> >
>>> >> >>> >>
>>> >> >>> >> On 2015-06-18 Thu 04:32, Xebar = Saram wrote:
>>> >> >>> >> > Hi Titus and thx so much f= or the answers!
>>> >> >>> >> >
>>> >> >>> >> > i will in the future use t= he github page to make requests.
>>> >> >>> >> >
>>> >> >>> >> > "The number of matche= s will be displayed in the mode line. "
>>> >> >>> >> >
>>> >> >>> >> > i see that now thx! :) the= problem was(is) that its colored
>>> black
>>> >> on
>>> >> >>> my
>>> >> >>> >> > black modline BG which mak= es it invisible ;-) i assume thats
>>> an
>>> >> helm
>>> >> >>> >> config
>>> >> >>> >> > i need to change
>>> >> >>> >> >
>>> >> >>> >> >
>>> >> >>> >> > "If you don=E2=80=99t= want to type these search expressions, you could
>>> >> >>> create a
>>> >> >>> >> > command that invokes helm-= bibtex with a default search
>>> expression
>>> >> and
>>> >> >>> >> that
>>> >> >>> >> > command could be bound to = a keyboard shortcut."
>>> >> >>> >> >
>>> >> >>> >> > that would be prefect for = me and a solution to my issue.
>>> would you
>>> >> >>> mind
>>> >> >>> >> > giving an example of such = a code chunk. unfortunately i dont
>>> know
>>> >> >>> elisp
>>> >> >>> >> though
>>> >> >>> >> > as john recommended i will= do my best this summer when the
>>> >> semester
>>> >> >>> ends
>>> >> >>> >> to
>>> >> >>> >> > try and pick it up :)
>>> >> >>> >>
>>> >> >>> >> Sure, here you go:
>>> >> >>> >>
>>> >> >>> >> #+BEGIN_SRC elisp
>>> >> >>> >> ;; Define helm-search with pred= efined search expression:
>>> >> >>> >> (defun helm-bibtex-my-publicati= ons ()
>>> >> >>> >>=C2=A0 =C2=A0"Search BibTeX= entries authored by Xebar Saram."
>>> >> >>> >>=C2=A0 =C2=A0(interactive)
>>> >> >>> >>=C2=A0 =C2=A0(helm :sources '= ;(helm-source-bibtex)
>>> >> >>> >>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0:full-frame t
>>> >> >>> >>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0:input "xebar saram"
>>> >> >>> >>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0:candidate-number-limit 500))
>>> >> >>> >>
>>> >> >>> >> ;; Bind this search function to= Ctrl-x p:
>>> >> >>> >> (global-set-key (kbd "C-x = p") 'helm-bibtex-my-publications)
>>> >> >>> >> #+END_SRC
>>> >> >>> >>
>>> >> >>> >> > i will definitely use your= tag system as you recommended,
>>> sounds
>>> >> >>> perfect
>>> >> >>> >> > for me
>>> >> >>> >>
>>> >> >>> >> The tag system also comes in ha= ndy when generating publication
>>> lists
>>> >> >>> for
>>> >> >>> >> CVs and web pages because BibTe= X does not distinguish between
>>> >> >>> conference
>>> >> >>> >> papers, posters, and talks.=C2= =A0 If you have tags for that, it=E2=80=99s
>>> >> relatively
>>> >> >>> >> easy to create separate section= s for these types of publications
>>> >> using
>>> >> >>> >> biblatex or bib2bib and bibtex2= html in the case of web pages.
>>> >> >>> >>
>>> >> >>> >> > thanks again for your kind= help and the amazing app ;-)
>>> >> >>> >>
>>> >> >>> >> You are welcome.
>>> >> >>> >>
>>> >> >>> >>=C2=A0 =C2=A0Titus
>>> >> >>> >>
>>> >> >>> >> >
>>> >> >>> >> > best
>>> >> >>> >> >
>>> >> >>> >> > Z
>>> >> >>> >> >
>>> >> >>> >> >
>>> >> >>> >> >
>>> >> >>> >> > On Wed, Jun 17, 2015 at 11= :02 PM, Titus von der Malsburg <
>>> >> >>> >> malsburg@posteo.de
>>> >> >>> >> >> wrote:
>>> >> >>> >> >
>>> >> >>> >> >>
>>> >> >>> >> >> On 2015-06-17 Wed 11:0= 8, Xebar Saram wrote:
>>> >> >>> >> >> > Hi Titus
>>> >> >>> >> >> >
>>> >> >>> >> >> > I have been explo= ring helm-bibtex a bit today and have some
>>> >> >>> questions.
>>> >> >>> >> >> btw
>>> >> >>> >> >> > is this the prefe= rred way to make requests/ask questions
>>> or is
>>> >> >>> >> >> > github preferred?=
>>> >> >>> >> >>
>>> >> >>> >> >> Helm-bibtex is not par= t of org (although it tries to work
>>> well
>>> >> with
>>> >> >>> >> >> org).=C2=A0 So I=E2=80= =99m not sure whether this list is the best place
>>> for
>>> >> >>> >> >> discussing it.=C2=A0 F= or now the issue tracker on Github might be
>>> a
>>> >> >>> better
>>> >> >>> >> >> option:
>>> >> >>> >> >>
>>> >> >>> >> >>=C2=A0 =C2=A0https://github.com/tmalsburg/helm-bibtex/issues
>>> >> >>> >> >>
>>> >> >>> >> >> > in any case i was= wondering a few things:
>>> >> >>> >> >> >
>>> >> >>> >> >> > 1. is it possible= to have custom sorting? i want all views
>>> to
>>> >> >>> sort by
>>> >> >>> >> >> > Author, year, mon= th
>>> >> >>> >> >>
>>> >> >>> >> >> I prefer to see the en= tries in the (inverse) order in which
>>> they
>>> >> >>> appear
>>> >> >>> >> >> in the BibTeX file.=C2= =A0 This way, recent additions show up at
>>> the
>>> >> >>> >> >> top.=C2=A0 However, I = agree that sorting would be useful (see
>>> issues
>>> >> #5
>>> >> >>> and
>>> >> >>> >> >> #21); it just doesn=E2= =80=99t have high priority for me.=C2=A0 Pull
>>> requests
>>> >> >>> welcome.
>>> >> >>> >> >>
>>> >> >>> >> >> > 2. i would really= like a way to have stored smart groups
>>> (like
>>> >> the
>>> >> >>> >> jabref
>>> >> >>> >> >> > dynamic groups if= your aware of that). that is for example
>>> >> create
>>> >> >>> a
>>> >> >>> >> group
>>> >> >>> >> >> > that auto selects= all publications i have (by my first/last
>>> >> name)
>>> >> >>> and
>>> >> >>> >> >> shows
>>> >> >>> >> >> > the count (in num= bers) of these publications.
>>> >> >>> >> >>
>>> >> >>> >> >> I=E2=80=99m not famili= ar with smart groups but it seems that all
>>> >> >>> helm-bibtex is
>>> >> >>> >> >> doing is giving you ve= ry flexible smart groups defined by
>>> your
>>> >> >>> search
>>> >> >>> >> >> expressions.=C2=A0 For= example, if you want a list of your
>>> >> publications,
>>> >> >>> you
>>> >> >>> >> >> can simple enter your = name.=C2=A0 And if you want a list of your
>>> >> >>> articles,
>>> >> >>> >> >> you can enter your nam= e + =E2=80=9Carticle=E2=80=9D.=C2=A0 If you want all your
>>> >> articles
>>> >> >>> from
>>> >> >>> >> >> 2010, enter your name = + =E2=80=9Carticles 2010=E2=80=9D.=C2=A0 And so on.=C2=A0 The
>>> number
>>> >> of
>>> >> >>> >> >> matches will be displa= yed in the mode line.=C2=A0 If you don=E2=80=99t
>>> want to
>>> >> >>> type
>>> >> >>> >> >> these search expressio= ns, you could create a command that
>>> invokes
>>> >> >>> >> >> helm-bibtex with a def= ault search expression and that command
>>> >> could
>>> >> >>> be
>>> >> >>> >> >> bound to a keyboard sh= ortcut.
>>> >> >>> >> >>
>>> >> >>> >> >> > Another example i= s a group to keep track of all the papers
>>> im
>>> >> >>> working
>>> >> >>> >> on
>>> >> >>> >> >> or
>>> >> >>> >> >> > invloved with by = matching keyword author and prep/*other
>>> key
>>> >> word
>>> >> >>> >> >>
>>> >> >>> >> >> I use two BibTeX field= s to tag entries: =E2=80=9Ckeywords=E2=80=9D for
>>> keywords
>>> >> >>> >> >> describing the content= of the paper (as usual) and =E2=80=9Ctags=E2=80=9D for
>>> >> meta
>>> >> >>> >> >> data.=C2=A0 Values tha= t I use in tags are =E2=80=9Cown=E2=80=9D, =E2=80=9Cmanuscript=E2=80=9D, >>> >> =E2=80=9Cposter=E2=80=9D,
>>> >> >>> >> >> =E2=80=9Ctalk=E2=80=9D= , =E2=80=A6 So if I want a list of all articles in progress, I
>>> >> search
>>> >> >>> for
>>> >> >>> >> >> =E2=80=9Cown manuscrip= t=E2=80=9D.=C2=A0 Since the tags field is non-standard, it
>>> has
>>> >> to
>>> >> >>> be
>>> >> >>> >> >> added to `helm-bibtex-= additional-search-fields`.
>>> >> >>> >> >>
>>> >> >>> >> >> Another solution would= be to use the pubstate field and to
>>> search
>>> >> >>> for
>>> >> >>> >> >> your name and =E2=80= =9Cforthcoming=E2=80=9D (add pubstate to
>>> >> >>> >> >> helm-bibtex-additional= -search-fields for this to work).
>>> >> >>> >> >>
>>> >> >>> >> >> > 3.is it possible to ass an = option to auto generate a
>>> bibkey
>>> >> for a
>>> >> >>> >> >> selected
>>> >> >>> >> >> > citation based on= user criteria such as
>>> >> author(date)short-title?
>>> >> >>> >> >>
>>> >> >>> >> >> Maintaining the conten= t of the BibTeX file not really in the
>>> >> scope
>>> >> >>> of
>>> >> >>> >> >> helm-bibtex (I prefer = to write my BibTeX entries by hand).
>>> >> Perhaps
>>> >> >>> >> >> org-ref or ebib can he= lp here?=C2=A0 Once you have a function that
>>> >> >>> generates
>>> >> >>> >> >> a new key and inserts = it in the BibTeX file, you can easily
>>> add
>>> >> it
>>> >> >>> to
>>> >> >>> >> >> the list of actions in= helm-bibtex.
>>> >> >>> >> >>
>>> >> >>> >> >> Hope that helps.
>>> >> >>> >> >>
>>> >> >>> >> >>=C2=A0 =C2=A0Titus
>>> >> >>> >> >>
>>> >> >>> >> >> > thx so much in ad= vance, you and john have given me
>>> confidence
>>> >> to
>>> >> >>> >> finally
>>> >> >>> >> >> > dive into the who= le latex/bibteX world
>>> >> >>> >> >> >
>>> >> >>> >> >> > best
>>> >> >>> >> >> >
>>> >> >>> >> >> > Z
>>> >> >>> >> >>
>>> >> >>> >> >>
>>> >> >>> >>
>>> >> >>> >>
>>> >> >>>
>>> >> >>>
>>> >> >>
>>> >>
>>> >>
>>>
>>> --
>>> Professor John Kitchin
>>> Doherty Hall A207F
>>> Department of Chemical Engineering
>>> Carnegie Mellon University
>>> Pittsburgh, PA 15213
>>> 412-268-78= 03
>>> @johnkitchin
>>> http://kitchingroup.cheme.cmu.edu
>>>
>>
>>

--
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu

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